Dive Analysis and Calibration

---

Documentation for package ‘diveMove’ version 1.6.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E F G L O P R S T misc

diveMove-package

Dive Analysis and Calibration

-- A --

as.data.frame-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
as.TDRspeed	Coerce, Extractor, and Replacement methods for class "TDR" objects
as.TDRspeed-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
austFilter	Filter satellite locations

-- B --

bec	Calculate bout ending criteria from model coefficients
bec-method	Calculate bout ending criteria from model coefficients
boutfreqs	Histogram of log-transformed frequencies
boutinit	Fit "broken stick" model to log frequency data for identification of bouts of behaviour
boutinit-method	Fit "broken stick" model to log frequency data for identification of bouts of behaviour
Bouts	Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
Bouts-class	Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
boutsCDF	Estimated cumulative frequency for two- or three-process Poisson mixture models
boutsNLSll	Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model
boutsNLSll-method	Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model

-- C --

calibrateDepth	Calibrate Depth and Generate a "TDRcalibrate" object
calibrateSpeed	Calibrate and build a "TDRcalibrate" object
ccData<-	Coerce, Extractor, and Replacement methods for class "TDR" objects
ccData<--method	Coerce, Extractor, and Replacement methods for class "TDR" objects
coerce-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
createTDR	Read comma-delimited file with "TDR" data

-- D --

depth<-	Coerce, Extractor, and Replacement methods for class "TDR" objects
depth<--method	Coerce, Extractor, and Replacement methods for class "TDR" objects
distSpeed	Calculate distance and speed between locations
diveModel	Class "diveModel" for representing a model for identifying dive phases
diveModel-class	Class "diveModel" for representing a model for identifying dive phases
diveMove	Dive Analysis and Calibration
dives	Sample of TDR data from a fur seal
diveStats	Per-dive statistics
divesTDR	Sample of TDR data from a fur seal
divesTDRzoc	Sample of TDR data from a fur seal

-- E --

extractDive	Extract Dives from "TDR" or "TDRcalibrate" Objects
extractDive-method	Extract Dives from "TDR" or "TDRcalibrate" Objects

-- F --

fitMLEbouts	Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
fitMLEbouts-method	Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
fitNLSbouts	Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression
fitNLSbouts-method	Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression

-- G --

getCCData	Coerce, Extractor, and Replacement methods for class "TDR" objects
getCCData-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
getDAct	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDAct-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDepth	Coerce, Extractor, and Replacement methods for class "TDR" objects
getDepth-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
getDiveDeriv	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveDeriv-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveModel	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveModel-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDPhaseLab	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDPhaseLab-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDtime	Coerce, Extractor, and Replacement methods for class "TDR" objects
getDtime-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
getFileName	Coerce, Extractor, and Replacement methods for class "TDR" objects
getFileName-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
getGAct	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getGAct-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getSpeed	Coerce, Extractor, and Replacement methods for class "TDR" objects
getSpeed-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
getSpeedCoef	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getSpeedCoef-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTDR	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTDR-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTime	Coerce, Extractor, and Replacement methods for class "TDR" objects
getTime-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
grpSpeedFilter	Filter satellite locations

-- L --

labelBouts	Label each vector element or matrix row with bout membership number
labelBouts-method	Label each vector element or matrix row with bout membership number

-- O --

oneDiveStats

Per-dive statistics

-- P --

plotBouts	Plot fitted Poisson mixture model and data
plotBouts-method	Plot fitted Poisson mixture model and data
plotBoutsCDF	Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotBoutsCDF-method	Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotDiveModel	Methods for plotting models of dive phases
plotDiveModel-method	Methods for plotting models of dive phases
plotTDR	Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotTDR-method	Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotZOC	Methods for visually assessing results of ZOC procedure
plotZOC-method	Methods for visually assessing results of ZOC procedure

-- R --

readLocs	Read comma-delimited file with location data
readTDR	Read comma-delimited file with "TDR" data
rmixexp	Generate samples from a mixture of exponential distributions
rmsDistFilter	Filter satellite locations
rqPlot	Plot of quantile regression for speed calibrations

-- S --

sealLocs	Ringed and Gray Seal ARGOS Satellite Location Data
show-method	Coerce, Extractor, and Replacement methods for class "TDR" objects
show-method	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
speed<-	Coerce, Extractor, and Replacement methods for class "TDR" objects
speed<--method	Coerce, Extractor, and Replacement methods for class "TDR" objects
stampDive	Per-dive statistics

-- T --

TDR	Classes "TDR" and "TDRspeed" for representing TDR information
TDR-accessors	Coerce, Extractor, and Replacement methods for class "TDR" objects
TDR-class	Classes "TDR" and "TDRspeed" for representing TDR information
TDR-methods	Coerce, Extractor, and Replacement methods for class "TDR" objects
TDRcalibrate	Class "TDRcalibrate" for dive analysis
TDRcalibrate-accessors	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
TDRcalibrate-class	Class "TDRcalibrate" for dive analysis
TDRcalibrate-methods	Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
TDRspeed	Classes "TDR" and "TDRspeed" for representing TDR information
TDRspeed-class	Classes "TDR" and "TDRspeed" for representing TDR information
timeBudget	Describe the Time Budget of Major Activities from "TDRcalibrate" object.
timeBudget-method	Describe the Time Budget of Major Activities from "TDRcalibrate" object.

-- misc --

.runquantile	Quantile of Moving Window
[-method	Coerce, Extractor, and Replacement methods for class "TDR" objects